Bladder Cancer

USD Bioinformatics

Bladder Cancer

Bladder Cancer

T1NP: T1 non progressive cancer

Patients have multiples recurrences of the disease without

developing muscle-invasive tumors

T1P: T1 progressive cancer

Patient’s disease develops into muscle invasive tumors and

becomes metastatic.

Once metastatic, cancer survival is around 5.4% at 5 years.

Through RNA Seq

Different gene expressions appeared between

Nonprogressive and Progressive bladder cancer.

Biomarkers that were identified in the future could also

help predict the pace of progression of muscle invasive

tumors using Formalin-Fixed and Paraffin-Embedded

samples.

How to achieve these result?

cDNA samples were sequenced on Illumina Genome

Analyzer II.

Sequences attained from Illumina were given by

CASAVA software

Reads attained were compared to the human

genome using Tophat

Reads were done using Cufflinks

Workflow of Reads

Quality Assessment

Alignment

Variant Identification

Variant Annotation

Visualization

CASAVA

Stands for Consensus Assessment of Sequence and

Variation software

Aligns reads, calls SNPs, and detects INDELs in

RNA sequencing data

Analyzes reads in 3 stages:

FASTQ file generation and simplify

Alignment to a reference genome

Variant detection and counting

TopHat

Fast splice junction mapper for RNA-Seq reads.

Aligns reads using Bowtie

Then analyzes the mapping results to identify splice

junctions between exons

Cufflink

Assembles transcripts

Estimates their abundances

Tests for differential expression and regulation

Conclusion

Tools work together to help clinicians analyze the

patient

Helps in making not precise but more accurate

predictions and diagnosis

Works Cited"CASAVA." Support. Illumina, n.d. Web. 27 June 2014.

<http://support.illumina.com/sequencing/sequencing_software/casava.ilmn>.

"CASAVA | Align reads, call SNPs and detect indels in DNA sequencing data |

Illumina." CASAVA | Align reads, call SNPs and detect indels in DNA

sequencing data | Illumina. Illumina, n.d. Web. 27 June 2014.

<http://www.illumina.com/informatics/sequencing-microarray-data-

analysis/casava.ilmn>.

Pachter, Lior, Steven Salzberg, and Barbara Wold. "Cufflinks." - Transcript assembly,

differential expression, and differential regulation for RNA-Seq. N.p., 26 Sept.

2009. Web. 27 June 2014. <http://cufflinks.cbcb.umd.edu/>.

Trapnell, Cole, Daehwan Kim, and Steven Salzberg. "TopHat." :: Center for

Bioinformatics and Computational Biology. John Hopkins University, 27 Oct.

2008. Web. 25 June 2014. <http://ccb.jhu.edu/software/tophat/index.shtml>.

Works CitedSharron Lin, Xuanhui, et al. "Differentiating Progressive From Nonprogressive T1 Bladder Cancer By

Gene Expression Profiling: Applying RNA-Sequencing Analysis On Archived

Specimens." Urologic Oncology 32.3 (2014): 327-336. Academic Search Premier. Web. 23

June 2014.